1
|
Bao L, Zhu Z, Ismail A, Zhu B, Anandan V, Whiteley M, Kitten T, Xu P. Experimental evolution of gene essentiality in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.600122. [PMID: 39071448 PMCID: PMC11275930 DOI: 10.1101/2024.07.16.600122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Essential gene products carry out fundamental cellular activities in interaction with other components. However, the lack of essential gene mutants and appropriate methodologies to link essential gene functions with their partners poses significant challenges. Here, we have generated deletion mutants in 32 genes previously identified as essential, with 23 mutants showing extremely slow growth in the SK36 strain of Streptococcus sanguinis. The 23 genes corresponding to these mutants encode components of diverse pathways, are widely conserved among bacteria, and are essential in many other bacterial species. Whole-genome sequencing of 243 independently evolved populations of these mutants has identified >1000 spontaneous suppressor mutations in experimental evolution. Many of these mutations define new gene and pathway relationships, such as F1Fo-ATPase/V1Vo-ATPase/TrkA1-H1 that were demonstrated across multiple Streptococcus species. Patterns of spontaneous mutations occurring in essential gene mutants differed from those found in wildtype. While gene duplications occurred rarely and appeared most often at later stages of evolution, substitutions, deletions, and insertions were prevalent in evolved populations. These essential gene deletion mutants and spontaneous mutations fixed in the mutant populations during evolution establish a foundation for understanding gene essentiality and the interaction of essential genes in networks.
Collapse
Affiliation(s)
- Liang Bao
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Zan Zhu
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Ahmed Ismail
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Bin Zhu
- Massey Cancer Center, Virginia Commonwealth University, Virginia, USA
| | - Vysakh Anandan
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Marvin Whiteley
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Georgia, USA
| | - Todd Kitten
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Ping Xu
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| |
Collapse
|
2
|
Lejeune C, Cornu D, Sago L, Redeker V, Virolle MJ. The stringent response is strongly activated in the antibiotic producing strain, Streptomyces coelicolor. Res Microbiol 2024; 175:104177. [PMID: 38159786 DOI: 10.1016/j.resmic.2023.104177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
S. lividans and S. coelicolor are phylogenetically closely related strains with different abilities to produce the same specialized metabolites. Previous studies revealed that the strong antibiotic producer, S. coelicolor, had a lower ability to assimilate nitrogen and phosphate than the weak producer, Streptomyces lividans, and this resulted into a lower growth rate. A comparative proteomic dataset was used to establish the consequences of these nutritional stresses on the abundance of proteins of the translational apparatus of these strains, grown in low and high phosphate availability. Our study revealed that most proteins of the translational apparatus were less abundant in S. coelicolor than in S. lividans whereas it was the opposite for ET-Tu 3 and a TrmA-like methyltransferase. The expression of the latter being known to be under the positive control of the stringent response whereas that of the other ribosomal proteins is under its negative control, this indicated the occurrence of a strong activation of the stringent response in S. coelicolor. Furthermore, in S. lividans, ribosomal proteins were more abundant in phosphate proficiency than in phosphate limitation suggesting that a limitation in phosphate, that was also shown to trigger RelA expression, contributes to the induction of the stringent response.
Collapse
Affiliation(s)
- Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Laila Sago
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Virginie Redeker
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France; Institut Francois Jacob, Molecular Imaging Center (MIRCen), Laboratory of Neurodegenerative Diseases, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique, Université Paris-Saclay, Fontenay-aux-Roses, France.
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| |
Collapse
|
3
|
Chakraborty A, Halder S, Kishore P, Saha D, Saha S, Sikder K, Basu A. The structure-function analysis of Obg-like GTPase proteins along the evolutionary tree from bacteria to humans. Genes Cells 2022; 27:469-481. [PMID: 35610748 PMCID: PMC9545696 DOI: 10.1111/gtc.12942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 11/28/2022]
Abstract
Obg proteins belong to P-loop guanine triphosphatase (GTPase) that are conserved from bacteria to humans. Like other GTPases, Obg cycles between guanine triphosphate (GTP) bound "on" state and guanine diphosphate (GDP)-bound "off" state, thereby controlling various cellular processes. Different members of this group have unique structural characteristics; a conserved glycine-rich N-terminal domain known as obg fold, a central conserved nucleotide binding domain, and a less conserved C-terminal domain of other functions. Obg is a ribosome dependent GTPase helps in ribosome maturation by interacting with several proteins of the 50S subunit of the ribosome. Obg proteins have been widely considered as a regulator of cellular functions, helping in DNA replication, cell division. Apart from that, this protein also takes part in various stress adaptation pathways like a stringent response, sporulation, and general stress response. In this particular review, the structural features of ObgE have been highlighted and how the structure plays important role in interacting with regulators like GTP, ppGpp that are crucial for executing biological function has been orchestrated. In particular, we believe that Obg-like proteins can provide a link between different global pathways that are necessary for fine-tuning cellular processes to maintain the cellular energy status.
Collapse
Affiliation(s)
- Asmita Chakraborty
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sheta Halder
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Purvi Kishore
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Disha Saha
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Sujata Saha
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Kunal Sikder
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Arnab Basu
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| |
Collapse
|
4
|
Ordóñez-Robles M, Rodríguez-García A, Martín JF. Genome-wide transcriptome response of Streptomyces tsukubaensis to N-acetylglucosamine: effect on tacrolimus biosynthesis. Microbiol Res 2018; 217:14-22. [DOI: 10.1016/j.micres.2018.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/04/2018] [Accepted: 08/29/2018] [Indexed: 11/29/2022]
|
5
|
Shahid MA, Marenda MS, Markham PF, Noormohammadi AH. Complementation of the Mycoplasma synoviae MS-H vaccine strain with wild-type obg influencing its growth characteristics. PLoS One 2018; 13:e0194528. [PMID: 29590172 PMCID: PMC5874028 DOI: 10.1371/journal.pone.0194528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 03/05/2018] [Indexed: 11/19/2022] Open
Abstract
The temperature-sensitive (ts+) Mycoplasma synoviae vaccine strain MS-H harbors a non-synonymous mutation which results in Glycine to Arginine substitution at position 123 in the highly conserved glycine-rich motif of Obg-fold in the GTP-binding protein Obg. In-silico analysis of the wild-type and mutant Obgs of M. synoviae has indicated that this amino acid substitution affects structure of the protein, potentially leading to abrogation of Obg function in vivo. Present study was conducted to develop the first expression vector for M. synoviae and to investigate the potential effect(s) of complementation of MS-H vaccine with the wild-type obg from 86079/7NS, the parent strain of MS-H. An oriC vector, pKS-VOTL, harboring the 86079/7NS obg gene, downstream of the variable lipoprotein haemagglutinin (vlhA) gene promoter, also cloned from 86079/7NS, was used to transform MS-H. The plasmid was localised at the chromosomal oriC locus of MS-H without any detectable integration at the chromosomal obg locus. Analysis of the MS-H transformants revealed abundant obg transcripts as well as Obg protein, when compared to the MS-H transformed with a similar vector, pMAS-LoriC, lacking obg coding sequence. The MS-H transformants complemented with wild-type Obg maintained their original temperature-sensitivity phenotype (consistent with MS-H vaccine) but, when compared to the MS-H transformed with pMAS-LoriC, had significantly higher (p < 0.05) growth rate and viability at the permissive (33°C) and non-permissive temperature (39.5°C), respectively. Analysis of Obg expression in MS-H and its wild-type parent strain revealed comparatively lower levels of Obg in MS-H. These results indicate that not only the mutation in Obg, but also the level of Obg expression, can confer functional abnormalities in the bacterial host. Furthermore, with the construction of first expression vector for M. synoviae, this study has set foundation for the development of recombinant vaccine(s) based on MS-H.
Collapse
Affiliation(s)
- Muhammad A. Shahid
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Marc S. Marenda
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Philip F. Markham
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Amir H. Noormohammadi
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| |
Collapse
|
6
|
Rice TSV3 Encoding Obg-Like GTPase Protein Is Essential for Chloroplast Development During the Early Leaf Stage Under Cold Stress. G3-GENES GENOMES GENETICS 2018; 8:253-263. [PMID: 29162684 PMCID: PMC5765353 DOI: 10.1534/g3.117.300249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Spo0B-associated GTP-binding (Obg) proteins are essential for the viability of nearly all bacteria. However, the detailed roles of Obg proteins in higher plants have not yet been elucidated. In this study, we identified a novel rice (Oryza sativa L.) thermo-sensitive virescent mutant (tsv3) that displayed an albino phenotype at 20° before the three-leaf stage while being a normal green at 32° or even at 20° after the four-leaf stage. The mutant phenotype was consistent with altered chlorophyll content and chloroplast structure in leaves. Map-based cloning and complementation experiments showed that TSV3 encoded a small GTP-binding protein. Subcellular localization studies revealed that TSV3 was localized to the chloroplasts. Expression of TSV3 was high in leaves and weak or undetectable in other tissues, suggesting a tissue-specific expression of TSV3 In the tsv3 mutant, expression levels of genes associated with the biogenesis of the chloroplast ribosome 50S subunit were severely decreased at the three-leaf stage under cold stress (20°), but could be recovered to normal levels at a higher temperature (32°). These observations suggest that the rice nuclear-encoded TSV3 plays important roles in chloroplast development at the early leaf stage under cold stress.
Collapse
|
7
|
Ordóñez-Robles M, Santos-Beneit F, Albillos SM, Liras P, Martín JF, Rodríguez-García A. Streptomyces tsukubaensis as a new model for carbon repression: transcriptomic response to tacrolimus repressing carbon sources. Appl Microbiol Biotechnol 2017; 101:8181-8195. [PMID: 28983826 DOI: 10.1007/s00253-017-8545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 11/26/2022]
Abstract
In this work, we identified glucose and glycerol as tacrolimus repressing carbon sources in the important species Streptomyces tsukubaensis. A genome-wide analysis of the transcriptomic response to glucose and glycerol additions was performed using microarray technology. The transcriptional time series obtained allowed us to compare the transcriptomic profiling of S. tsukubaensis growing under tacrolimus producing and non-producing conditions. The analysis revealed important and different metabolic changes after the additions and a lack of transcriptional activation of the fkb cluster. In addition, we detected important differences in the transcriptional response to glucose between S. tsukubaensis and the model species Streptomyces coelicolor. A number of genes encoding key players of morphological and biochemical differentiation were strongly and permanently downregulated by the carbon sources. Finally, we identified several genes showing transcriptional profiles highly correlated to that of the tacrolimus biosynthetic pathway regulator FkbN that might be potential candidates for the improvement of tacrolimus production.
Collapse
Affiliation(s)
- María Ordóñez-Robles
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Fernando Santos-Beneit
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Silvia M Albillos
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
- Departamento de Biotecnología y Ciencia de los Alimentos, Facultad de Ciencias, Universidad de Burgos, 09001, Burgos, Spain
| | - Paloma Liras
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Juan F Martín
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Antonio Rodríguez-García
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain.
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain.
| |
Collapse
|
8
|
Schellhaus AK, Moreno-Andrés D, Chugh M, Yokoyama H, Moschopoulou A, De S, Bono F, Hipp K, Schäffer E, Antonin W. Developmentally Regulated GTP binding protein 1 (DRG1) controls microtubule dynamics. Sci Rep 2017; 7:9996. [PMID: 28855639 PMCID: PMC5577222 DOI: 10.1038/s41598-017-10088-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/03/2017] [Indexed: 11/15/2022] Open
Abstract
The mitotic spindle, essential for segregating the sister chromatids into the two evolving daughter cells, is composed of highly dynamic cytoskeletal filaments, the microtubules. The dynamics of microtubules are regulated by numerous microtubule associated proteins. We identify here Developmentally regulated GTP binding protein 1 (DRG1) as a microtubule binding protein with diverse microtubule-associated functions. In vitro, DRG1 can diffuse on microtubules, promote their polymerization, drive microtubule formation into bundles, and stabilize microtubules. HeLa cells with reduced DRG1 levels show delayed progression from prophase to anaphase because spindle formation is slowed down. To perform its microtubule-associated functions, DRG1, although being a GTPase, does not require GTP hydrolysis. However, all domains are required as truncated versions show none of the mentioned activities besides microtubule binding.
Collapse
Affiliation(s)
- Anna Katharina Schellhaus
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076, Tübingen, Germany.,Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074, Aachen, Germany
| | - Daniel Moreno-Andrés
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076, Tübingen, Germany.,Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074, Aachen, Germany
| | - Mayank Chugh
- Cellular Nanoscience, Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Hideki Yokoyama
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076, Tübingen, Germany.,Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074, Aachen, Germany
| | - Athina Moschopoulou
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076, Tübingen, Germany
| | - Suman De
- Cellular Nanoscience, Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Fulvia Bono
- Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076, Tübingen, Germany
| | - Katharina Hipp
- Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076, Tübingen, Germany
| | - Erik Schäffer
- Cellular Nanoscience, Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076, Tübingen, Germany. .,Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074, Aachen, Germany.
| |
Collapse
|
9
|
Gkekas S, Singh RK, Shkumatov AV, Messens J, Fauvart M, Verstraeten N, Michiels J, Versées W. Structural and biochemical analysis of Escherichia coli ObgE, a central regulator of bacterial persistence. J Biol Chem 2017; 292:5871-5883. [PMID: 28223358 DOI: 10.1074/jbc.m116.761809] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/03/2017] [Indexed: 12/28/2022] Open
Abstract
The Obg protein family belongs to the TRAFAC (translation factor) class of P-loop GTPases and is conserved from bacteria to eukaryotes. Essential roles in many different cellular processes have been suggested for the Obg protein from Escherichia coli (ObgE), and we recently showed that it is a central regulator of bacterial persistence. Here, we report the first crystal structure of ObgE at 1.85-Å resolution in the GDP-bound state, showing the characteristic N-terminal domain and a central G domain that are common to all Obg proteins. ObgE also contains an intrinsically disordered C-terminal domain, and we show here that this domain specifically contributed to GTP binding, whereas it did not influence GDP binding or GTP hydrolysis. Biophysical analysis, using small angle X-ray scattering and multi-angle light scattering experiments, revealed that ObgE is a monomer in solution, regardless of the bound nucleotide. In contrast to recent suggestions, our biochemical analyses further indicate that ObgE is neither activated by K+ ions nor by homodimerization. However, the ObgE GTPase activity was stimulated upon binding to the ribosome, confirming the ribosome-dependent GTPase activity of the Obg family. Combined, our data represent an important step toward further unraveling the detailed molecular mechanism of ObgE, which might pave the way to further studies into how this GTPase regulates bacterial physiology, including persistence.
Collapse
Affiliation(s)
- Sotirios Gkekas
- From the Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels.,the VIB-VUB Center for Structural Biology, 1050 Brussels
| | - Ranjan Kumar Singh
- From the Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels.,the VIB-VUB Center for Structural Biology, 1050 Brussels
| | - Alexander V Shkumatov
- From the Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels.,the VIB-VUB Center for Structural Biology, 1050 Brussels
| | - Joris Messens
- From the Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels.,the VIB-VUB Center for Structural Biology, 1050 Brussels
| | - Maarten Fauvart
- the Centre of Microbial and Plant Genetics, KU Leuven, University of Leuven, 3001 Leuven, and.,the Department of Life Science Technologies, Smart Systems and Emerging Technologies Unit, IMEC, 3001 Leuven, Belgium
| | - Natalie Verstraeten
- the Centre of Microbial and Plant Genetics, KU Leuven, University of Leuven, 3001 Leuven, and
| | - Jan Michiels
- the Centre of Microbial and Plant Genetics, KU Leuven, University of Leuven, 3001 Leuven, and
| | - Wim Versées
- From the Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, .,the VIB-VUB Center for Structural Biology, 1050 Brussels
| |
Collapse
|
10
|
Chen J, Deng F, Deng M, Han J, Chen J, Wang L, Yan S, Tong K, Liu F, Tian M. Identification and Characterization of a Chloroplast-Targeted Obg GTPase in Dendrobium officinale. DNA Cell Biol 2016; 35:802-811. [PMID: 27710025 DOI: 10.1089/dna.2016.3413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bacterial homologous chloroplast-targeted Obg GTPases (ObgCs) belong to the plant-typical Obg group, which is involved in diverse physiological processes during chloroplast development. However, the evolutionarily conserved function of ObgC in plants remains elusive and requires further investigation. In this study, we identified DoObgC from an epiphytic plant Dendrobium officinale and demonstrated the characteristics of DoObgC. Sequence analysis indicated that DoObgC is highly conserved with other plant ObgCs, which contain the chloroplast transit peptide (cTP), Obg fold, G domain, and OCT regions. The C terminus of DoObgC lacking the chloroplast-targeting cTP region, DoObgCΔ1-160, showed strong similarity to ObgE and other bacterial Obgs. Overexpression of DoObgCΔ1-160 in Escherichia coli caused slow cell growth and an increased number of elongated cells. This phenotype was consistent with the phenotype of cells overexpressing ObgE. Furthermore, the expression of recombinant DoObgCΔ1-160 enhanced the cell persistence of E. coli to streptomycin. Results of transient expression assays revealed that DoObgC was localized to chloroplasts. Moreover, we demonstrated that DoObgC could rescue the embryotic lethal phenotype of the Arabidopsis obgc-t mutant, suggesting that DoObgC is a functional homolog to Arabidopsis AtObgC in D. officinale. Gene expression profiles showed that DoObgC was expressed in leaf-specific and light-dependent patterns and that DoObgC responded to wounding treatments. Our previous and present studies reveal that ObgC has an evolutionarily conserved role in ribosome biogenesis to adapt chloroplast development to the environment.
Collapse
Affiliation(s)
- Ji Chen
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Feng Deng
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Mengsheng Deng
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Jincheng Han
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Jianbin Chen
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Li Wang
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Shen Yan
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Kai Tong
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Fan Liu
- 1 Agronomy College, Sichuan Agricultural University , Chengdu, China
| | - Mengliang Tian
- 2 Institute for New Rural Development, Sichuan Agricultural University , Yaan, China
| |
Collapse
|
11
|
Chatterjee A, Datta PP. Intrinsic GTPase activity of a ribosomal maturation protein CgtA is associated with its inter-domain movement: insights from MD simulations and biochemical studies. J Biomol Struct Dyn 2016; 35:2578-2587. [PMID: 27677930 DOI: 10.1080/07391102.2016.1224732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ananya Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Partha P. Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| |
Collapse
|
12
|
Shao W, Zhang Y, Wang J, Lv C, Chen C. BcMtg2 is required for multiple stress tolerance, vegetative development and virulence in Botrytis cinerea. Sci Rep 2016; 6:28673. [PMID: 27346661 PMCID: PMC4921815 DOI: 10.1038/srep28673] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/06/2016] [Indexed: 01/05/2023] Open
Abstract
In Saccharomyces cerevisiae, the Mtg2 gene encodes the Obg protein, which has an important function in assembling ribosomal subunits. However, little is known about the role of the Obg GTPase in filamentous fungi. In this study, we identified an Mtg2 ortholog, BcMtg2, in B. cinerea. The BcMtg2 deletion mutant showed a defect in spore production, conidial germination and sclerotial formation. Additionally, the mutant increased sensitivity to various environmental stresses. The BcMtg2 mutant exhibited dramatically decreased virulence on host plant tissues. BcMtg2 mutant showed increased sensitivity to osmotic and oxidative stresses, and to Congo red (cell wall stress agent). In the yeast complement assay, growth defects of yeast BY4741ΔMTG2 mutant were partly restored by genetic complementation of BcMtg2 under these environmental stresses. Additionally, compared with the parental strain and complement strain, the BcMtg2 deletion mutant displayed a minor glycerol response to osmosis stress. These defective phenotypes were recovered in the complement strain ΔBcMtg2C, which was created by adding the wild-type BcMtg2 gene to the ΔBcMtg2 mutant. The results of this study indicate that BcMtg2 has a necessary role in asexual development, environmental stress response and pathogenicity in B. cinerea.
Collapse
Affiliation(s)
- Wenyong Shao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chiyuan Lv
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changjun Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
13
|
Bonventre JA, Zielke RA, Korotkov KV, Sikora AE. Targeting an Essential GTPase Obg for the Development of Broad-Spectrum Antibiotics. PLoS One 2016; 11:e0148222. [PMID: 26848972 PMCID: PMC4743925 DOI: 10.1371/journal.pone.0148222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/14/2016] [Indexed: 11/19/2022] Open
Abstract
A promising new drug target for the development of novel broad-spectrum antibiotics is the highly conserved small GTPase Obg (YhbZ, CgtA), a protein essential for the survival of all bacteria including Neisseria gonorrhoeae (GC). GC is the agent of gonorrhea, a prevalent sexually transmitted disease resulting in serious consequences on reproductive and neonatal health. A preventive anti-gonorrhea vaccine does not exist, and options for effective antibiotic treatments are increasingly limited. To address the dire need for alternative antimicrobial strategies, we have designed and optimized a 384-well GTPase assay to identify inhibitors of Obg using as a model Obg protein from GC, ObgGC. The assay was validated with a pilot screen of 40,000 compounds and achieved an average Z’ value of 0.58 ± 0.02, which suggests a robust assay amenable to high-throughput screening. We developed secondary assessments for identified lead compounds that utilize the interaction between ObgGC and fluorescent guanine nucleotide analogs, mant-GTP and mant-GDP, and an ObgGC variant with multiple alterations in the G-domains that prevent nucleotide binding. To evaluate the broad-spectrum potential of ObgGC inhibitors, Obg proteins of Klebsiella pneumoniae and methicillin-resistant Staphylococcus aureus were assessed using the colorimetric and fluorescence-based activity assays. These approaches can be useful in identifying broad-spectrum Obg inhibitors and advancing the therapeutic battle against multidrug resistant bacteria.
Collapse
Affiliation(s)
- Josephine A. Bonventre
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97330, United States of America
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97330, United States of America
| | - Konstantin V. Korotkov
- Department of Molecular and Cellular Biochemistry, and Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, United States of America
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97330, United States of America
- * E-mail:
| |
Collapse
|
14
|
Gallo G, Renzone G, Palazzotto E, Monciardini P, Arena S, Faddetta T, Giardina A, Alduina R, Weber T, Sangiorgi F, Russo A, Spinelli G, Sosio M, Scaloni A, Puglia AM. Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024. BMC Genomics 2016; 17:42. [PMID: 26754974 PMCID: PMC4709908 DOI: 10.1186/s12864-016-2369-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 01/06/2016] [Indexed: 11/24/2022] Open
Abstract
Background The filamentous actinomycete Microbispora ATCC-PTA-5024 produces the lantibiotic NAI-107, which is an antibiotic peptide effective against multidrug-resistant Gram-positive bacteria. In actinomycetes, antibiotic production is often associated with a physiological differentiation program controlled by a complex regulatory and metabolic network that may be elucidated by the integration of genomic, proteomic and bioinformatic tools. Accordingly, an extensive evaluation of the proteomic changes associated with NAI-107 production was performed on Microbispora ATCC-PTA-5024 by combining two-dimensional difference in gel electrophoresis, mass spectrometry and gene ontology approaches. Results Microbispora ATCC-PTA-5024 cultivations in a complex medium were characterized by stages of biomass accumulation (A) followed by biomass yield decline (D). NAI-107 production started at 90 h (A stage), reached a maximum at 140 h (D stage) and decreased thereafter. To reveal patterns of differentially represented proteins associated with NAI-107 production onset and maintenance, differential proteomic analyses were carried-out on biomass samples collected: i) before (66 h) and during (90 h) NAI-107 production at A stage; ii) during three time-points (117, 140, and 162 h) at D stage characterized by different profiles of NAI-107 yield accumulation (117 and 140 h) and decrement (162 h). Regulatory, metabolic and unknown-function proteins, were identified and functionally clustered, revealing that nutritional signals, regulatory cascades and primary metabolism shift-down trigger the accumulation of protein components involved in nitrogen and phosphate metabolism, cell wall biosynthesis/maturation, lipid metabolism, osmotic stress response, multi-drug resistance, and NAI-107 transport. The stimulating role on physiological differentiation of a TetR-like regulator, originally identified in this study, was confirmed by the construction of an over-expressing strain. Finally, the possible role of cellular response to membrane stability alterations and of multi-drug resistance ABC transporters as additional self-resistance mechanisms toward the lantibiotic was confirmed by proteomic and confocal microscopy experiments on a Microbispora ATCC-PTA-5024 lantibiotic-null producer strain which was exposed to an externally-added amount of NAI-107 during growth. Conclusion This study provides a net contribution to the elucidation of the regulatory, metabolic and molecular patterns controlling physiological differentiation in Microbispora ATCC-PTA-5024, supporting the relevance of proteomics in revealing protein players of antibiotic biosynthesis in actinomycetes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2369-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Giuseppe Gallo
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, 90128, Palermo, Italy.
| | - Giovanni Renzone
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy
| | - Emilia Palazzotto
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, 90128, Palermo, Italy
| | | | - Simona Arena
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy
| | - Teresa Faddetta
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, 90128, Palermo, Italy
| | - Anna Giardina
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, 90128, Palermo, Italy
| | - Rosa Alduina
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, 90128, Palermo, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark.,German Center for Infection Research (DZIF) partner site Tübingen, 72074, Tübingen, Germany
| | - Fabio Sangiorgi
- Sistema Informativo di Ateneo (SIA), Area Servizi di Rete, University of Palermo, 90128, Palermo, Italy
| | - Alessandro Russo
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, 90128, Palermo, Italy
| | - Giovanni Spinelli
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, 90128, Palermo, Italy
| | | | - Andrea Scaloni
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, 90128, Palermo, Italy
| |
Collapse
|
15
|
Sandoval-Calderón M, Nguyen DD, Kapono CA, Herron P, Dorrestein PC, Sohlenkamp C. Plasticity of Streptomyces coelicolor Membrane Composition Under Different Growth Conditions and During Development. Front Microbiol 2015; 6:1465. [PMID: 26733994 PMCID: PMC4686642 DOI: 10.3389/fmicb.2015.01465] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/07/2015] [Indexed: 01/08/2023] Open
Abstract
Streptomyces coelicolor is a model actinomycete that is well known for the diversity of its secondary metabolism and its complex life cycle. As a soil inhabitant, it is exposed to heterogeneous and frequently changing environmental circumstances. In the present work, we studied the effect of diverse growth conditions and phosphate depletion on its lipid profile and the relationship between membrane lipid composition and development in S. coelicolor. The lipid profile from cultures grown on solid media, which is closer to the natural habitat of this microorganism, does not resemble the previously reported lipid composition from liquid grown cultures of S. coelicolor. Wide variations were also observed across different media, growth phases, and developmental stages indicating active membrane remodeling. Ornithine lipids (OL) are phosphorus-free polar lipids that were accumulated mainly during sporulation stages, but were also major components of the membrane under phosphorus limitation. In contrast, phosphatidylethanolamine, which had been reported as one of the major polar lipids in the genus Streptomyces, is almost absent under these conditions. We identified one of the genes responsible for the synthesis of OL (SCO0921) and found that its inactivation causes the absence of OL, precocious morphological development and actinorhodin production. Our observations indicate a remarkable plasticity of the membrane composition in this bacterial species, reveal a higher metabolic complexity than expected, and suggest a relationship between cytoplasmic membrane components and the differentiation programs in S. coelicolor.
Collapse
Affiliation(s)
| | - Don D Nguyen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla CA, USA
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla CA, USA
| | - Paul Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow, UK
| | - Pieter C Dorrestein
- Department of Chemistry and Biochemistry, University of California, San Diego, La JollaCA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La JollaCA, USA
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| |
Collapse
|
16
|
Zielke RA, Wierzbicki IH, Baarda BI, Sikora AE. The Neisseria gonorrhoeae Obg protein is an essential ribosome-associated GTPase and a potential drug target. BMC Microbiol 2015; 15:129. [PMID: 26122105 PMCID: PMC4487204 DOI: 10.1186/s12866-015-0453-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background Neisseria gonorrhoeae (GC) is a Gram-negative pathogen that most commonly infects mucosal surfaces, causing sexually transmitted urethritis in men and endocervicitis in women. Serious complications associated with these infections are frequent and include pelvic inflammatory disease, ectopic pregnancy, and infertility. The incidence of gonorrhea cases remains high globally while antibiotic treatment options, the sole counter measures against gonorrhea, are declining due to the remarkable ability of GC to acquire resistance. Evaluating of potential drug targets is essential to provide opportunities for developing antimicrobials with new mechanisms of action. We propose the GC Obg protein, belonging to the Obg/CgtA GTPase subfamily, as a potential target for the development of therapeutic interventions against gonorrhea, and in this study perform its initial functional and biochemical characterization. Results We report that NGO1990 encodes Obg protein, which is an essential factor for GC viability, associates predominantly with the large 50S ribosomal subunit, and is stably expressed under conditions relevant to infection of the human host. The anti-Obg antisera cross-reacts with a panel of contemporary GC clinical isolates, demonstrating the ubiquitous nature of Obg. The cellular levels of Obg reach a maximum in the early logarithmic phase and remain constant throughout bacterial growth. The in vitro binding and hydrolysis of the fluorescent guanine nucleotide analogs mant-GTP and mant-GDP by recombinant wild type and T192AT193A mutated variants of Obg are also assessed. Conclusions Characterization of the GC Obg at the molecular and functional levels presented herein may facilitate the future targeting of this protein with small molecule inhibitors and the evaluation of identified lead compounds for bactericidal activity against GC and other drug-resistant bacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0453-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Igor H Wierzbicki
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Benjamin I Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| |
Collapse
|
17
|
Chen J, Bang WY, Lee Y, Kim S, Lee KW, Kim SW, Son YS, Kim DW, Akhter S, Bahk JD. AtObgC-AtRSH1 interaction may play a vital role in stress response signal transduction in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 74:176-84. [PMID: 24308987 DOI: 10.1016/j.plaphy.2013.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 10/16/2013] [Indexed: 05/24/2023]
Abstract
The interaction of Obg (Spo0B-associated GTP-binding protein) GTPase and SpoT, which is a bifunctional ppGpp (guanosine 3',5'-bispyrophosphate) hydrolase/synthetase, is vital for the modulation of intracellular ppGpp levels during bacterial responses to environmental cues. It has been recently reported that the ppGpp level is also inducible by various stresses in the chloroplasts of plant cells. However, the function of the Obg-SpoT interaction in plants remains elusive. The results from the present and previous studies suggest that AtRSH1 is a putative bacterial SpoT homolog in Arabidopsis and that its transcription levels are responsive to wounding and salt stresses. In this study, we used a yeast two-hybrid analysis to map the regions required for the AtObgC-AtRSH1 interaction. Moreover, protein-protein docking simulations revealed reasonable geometric and electrostatic complementarity in the binding surfaces of the two proteins. The data support our experimental results, which suggest that the conserved domains in AtObgC and the N terminus of AtRSH1 containing the TGS domain contribute to their interaction. In addition, quantitative real-time PCR (qRT-PCR) analyses showed that the expression of AtObgC and AtRSH1 exhibit a similar inhibition pattern under wounding and salt-stress conditions, but the inhibition pattern was not greatly influenced by the presence or absence of light. Based on in vivo analyses, we further confirmed that the AtRSH1 and AtObgC proteins similarly localize in chloroplasts. Based on these results, we propose that the AtObgC-AtRSH1 interaction plays a vital role in ppGpp-mediated stress responses in chloroplasts.
Collapse
Affiliation(s)
- Ji Chen
- Agronomy College, Sichuan Agricultural University, Chengdu 611130, China; Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Woo Young Bang
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-2133, USA
| | - Yuno Lee
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Songmi Kim
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Se Won Kim
- Green Bio Research Center, Cabbage Genomics Assisted Breeding Supporting Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Korea
| | - Young Sim Son
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Dae Won Kim
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Salina Akhter
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jeong Dong Bahk
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea.
| |
Collapse
|
18
|
Chen Y, Zhu H, Zheng G, Jiang W, Lu Y. Functional analysis of TetR-family regulator AmtRsav in Streptomyces avermitilis. MICROBIOLOGY-SGM 2013; 159:2571-2583. [PMID: 24068239 DOI: 10.1099/mic.0.071449-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In actinomycetes, two main regulators, the OmpR-like GlnR and the TetR-type AmtR, have been identified as the central regulators for nitrogen metabolism. GlnR-mediated regulation was previously identified in different actinomycetes except for members of the genus Corynebacterium, in which AmtR plays a predominant role in nitrogen metabolism. Interestingly, some actinomycetes (e.g. Streptomyces avermitilis) harbour both glnR- and amtR-homologous genes in the chromosome. Thus, it will be interesting to determine how these two different types of regulators function together in nitrogen regulation of these strains. In this study, AmtRsav (sav_6701) in S. avermitilis, the homologue of AmtR from Corynebacterium glutamicum, was functionally characterized. We showed, by real-time reverse transcription (RT)-PCR (qPCR) in combination with electrophoretic mobility shift assays (EMSAs), that gene cluster sav_6697-6700 encoding a putative amidase, a urea carboxylase and two hypothetical proteins, respectively, and sav_6709 encoding a probable amino acid permease are under the direct control of AmtRsav. Using approaches of comparative analysis combined with site-directed DNA mutagenesis, the AmtRsav binding sites in the respective intergenic regions of sav_6700/6701 and sav_6709/6710 were defined. By genome screening coupled with EMSAs, two novel AmtRsav binding sites were identified. Taken together, AmtRsav seems to play a marginal role in regulation of nitrogen metabolism of S. avermitilis.
Collapse
Affiliation(s)
- Yunliang Chen
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China.,Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Hong Zhu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Guosong Zheng
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Yinhua Lu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| |
Collapse
|
19
|
Ishikawa K, Ito K, Inoue JI, Semba K. Cell growth control by stable Rbg2/Gir2 complex formation under amino acid starvation. Genes Cells 2013; 18:859-72. [PMID: 23899355 DOI: 10.1111/gtc.12082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/02/2013] [Indexed: 11/28/2022]
Abstract
The molecular fine-tuning mechanisms underlying adaptive responses to environmental stresses in eukaryotes remain largely unknown. Here, we report on a novel stress-induced cell growth control mechanism involving a highly conserved complex containing Rbg2 and Gir2 subunits, which are the budding yeast orthologs of human Drg2 and Dfrp2, respectively. We found that the complex is responsible for efficient cell growth under amino acid starvation. Using native PAGE analyses, we observed that, individually, Rbg2 and Gir2 were labile proteins. However, they formed a complex that stabilized each other, and this stability became significantly enhanced after amino acid starvation. We observed that the stabilization of the complex was strictly dependent on GDP or GTP binding to Rbg2. A point mutation (S77N) that inactivated nucleotide binding impaired formation of the complex and disrupted the stress-induced cell growth. Interestingly, the complex bound the translational activator Gcn1 in a dose-dependent manner according to the stress level, suggesting a dynamic association with the cellular translational machinery. We propose that the Rbg2/Gir2 complex is a modulator that maintains cellular homoeostasis, thus promoting the survival of eukaryotic organisms in stressful environments.
Collapse
Affiliation(s)
- Kosuke Ishikawa
- Departments of Life Science & Medical Bio-Science, Waseda University, 2-2, Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | | | | | | |
Collapse
|
20
|
Kint C, Verstraeten N, Hofkens J, Fauvart M, Michiels J. Bacterial Obg proteins: GTPases at the nexus of protein and DNA synthesis. Crit Rev Microbiol 2013; 40:207-24. [PMID: 23537324 DOI: 10.3109/1040841x.2013.776510] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Obg proteins (also known as ObgE, YhbZ and CgtA) are conserved P-loop GTPases, essential for growth in bacteria. Like other GTPases, Obg proteins cycle between a GTP-bound ON and a GDP-bound OFF state, thereby controlling cellular processes. Interestingly, the in vitro biochemical properties of Obg proteins suggest that they act as sensors for the cellular GDP/GTP pools and adjust their activity according to the cellular energy status. Obg proteins have been attributed a host of cellular functions, including roles in essential cellular processes (DNA replication, ribosome maturation) and roles in different stress adaptation pathways (stringent response, sporulation, general stress response). This review summarizes the current knowledge on Obg activity and function. Furthermore, we present a model that integrates the different functions of Obg by assigning it a fundamental role in cellular physiology, at the hub of protein and DNA synthesis. In particular, we believe that Obg proteins might provide a connection between different global pathways in order to fine-tune cellular processes in response to a given energy status.
Collapse
Affiliation(s)
- Cyrielle Kint
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven , Kasteelpark Arenberg 20, 3001 Heverlee , Kasteelpark Arenberg 20, 3001 Heverlee and
| | | | | | | | | |
Collapse
|
21
|
Abstract
The ribosome is an RNA- and protein-based macromolecule having multiple functional domains to facilitate protein synthesis, and it is synthesized through multiple steps including transcription, stepwise cleavages of the primary transcript, modifications of ribosomal proteins and RNAs and assemblies of ribosomal proteins with rRNAs. This process requires dozens of trans-acting factors including GTP- and ATP-binding proteins to overcome several energy-consuming steps. Despite accumulation of genetic, biochemical and structural data, the entire process of bacterial ribosome synthesis remains elusive. Here, we review GTPases involved in bacterial ribosome maturation.
Collapse
Affiliation(s)
- Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | | | | |
Collapse
|
22
|
Kint CI, Verstraeten N, Wens I, Liebens VR, Hofkens J, Versées W, Fauvart M, Michiels J. The Escherichia coli GTPase ObgE modulates hydroxyl radical levels in response to DNA replication fork arrest. FEBS J 2012; 279:3692-3704. [PMID: 22863262 DOI: 10.1111/j.1742-4658.2012.08731.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Obg proteins are universally conserved GTP-binding proteins that are essential for viability in bacteria. Homologs in different organisms are involved in various cellular processes, including DNA replication. The goal of this study was to analyse the structure-function relationship of Escherichia coli ObgE with regard to DNA replication in general and sensitivity to stalled replication forks in particular. Defined C-terminal chromosomal deletion mutants of obgE were constructed and tested for sensitivity to the replication inhibitor hydroxyurea. The ObgE C-terminal domain was shown to be dispensable for normal growth of E.coli. However, a region within this domain is involved in the cellular response to replication fork stress. In addition, a mutant obgE over-expression library was constructed by error-prone PCR and screened for increased hydroxyurea sensitivity. ObgE proteins with substitutions L159Q, G163V, P168V, G216A or R237C, located within distinct domains of ObgE, display dominant-negative effects leading to hydroxyurea hypersensitivity when over-expressed. These effects are abolished in strains with a single deletion of the iron transporter TonB or combined deletions the toxin/antitoxin modules RelBE/MazEF, strains both of which have been shown to be involved in a pathway that stimulates hydroxyl radical formation following hydroxyurea treatment. Moreover, the observed dominant-negative effects are lost in the presence of the hydroxyl radical scavenger thiourea. Together, these results indicate involvement of hydroxyl radical toxicity in ObgE-mediated protection against replication fork stress.
Collapse
Affiliation(s)
- Cyrielle I Kint
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Inez Wens
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Veerle R Liebens
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Johan Hofkens
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Wim Versées
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium Department of Chemistry, Katholieke Universiteit Leuven, Heverlee, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Belgium Department of Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| |
Collapse
|
23
|
Bang WY, Chen J, Jeong IS, Kim SW, Kim CW, Jung HS, Lee KH, Kweon HS, Yoko I, Shiina T, Bahk JD. Functional characterization of ObgC in ribosome biogenesis during chloroplast development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:122-34. [PMID: 22380942 DOI: 10.1111/j.1365-313x.2012.04976.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The Spo0B-associated GTP-binding protein (Obg) GTPase, essential for bacterial viability, is also conserved in eukaryotes, but its primary role in eukaryotes remains unknown. Here, our functional characterization of Arabidopsis and rice obgc mutants strongly underlines the evolutionarily conserved role of eukaryotic Obgs in organellar ribosome biogenesis. The mutants exhibited a chlorotic phenotype, caused by retarded chloroplast development. A plastid DNA macroarray revealed a plastid-encoded RNA polymerase (PEP) deficiency in an obgc mutant, caused by incompleteness of the PEP complex, as its western blot exhibited reduced levels of RpoA protein, a component of PEP. Plastid rRNA profiling indicated that plastid rRNA processing is defective in obgc mutants, probably resulting in impaired ribosome biogenesis and, in turn, in reduced levels of RpoA protein. RNA co-immunoprecipitation revealed that ObgC specifically co-precipitates with 23S rRNA in vivo. These findings indicate that ObgC functions primarily in plastid ribosome biogenesis during chloroplast development. Furthermore, complementation analysis can provide new insights into the functional modes of three ObgC domains, including the Obg fold, G domain and OCT.
Collapse
Affiliation(s)
- Woo Young Bang
- Swine Science and Technology Center, Gyeongnam National University of Science and Technology-GNTECH, Jinju 660-758, Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Ochi K, Nishizawa T, Inaoka T, Yamada A, Hashimoto K, Hosaka T, Okamoto S, Ozeki Y. Heterologous expression of a plant RelA-SpoT homologue results in increased stress tolerance in Saccharomyces cerevisiae by accumulation of the bacterial alarmone ppGpp. MICROBIOLOGY-SGM 2012; 158:2213-2224. [PMID: 22679107 DOI: 10.1099/mic.0.057638-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The bacterial alarmone ppGpp is present only in bacteria and the chloroplasts of plants, but not in mammalian cells or eukaryotic micro-organisms such as yeasts and fungi. The importance of the ppGpp signalling system in eukaryotes has therefore been largely overlooked. Here, we demonstrated that heterologous expression of a relA-spoT homologue (Sj-RSH) isolated from the halophilic plant Suaeda japonica in the yeast Saccharomyces cerevisiae results in accumulation of ppGpp, accompanied by enhancement of tolerance against various stress stimuli, such as osmotic stress, ethanol, hydrogen peroxide, high temperature and freezing. Unlike bacterial ppGpp accumulation, ppGpp was accumulated in the early growth phase but not in the late growth phase. Moreover, nutritional downshift resulted in a decrease in ppGpp level, suggesting that the observed Sj-RSH activity to synthesize ppGpp is not starvation-dependent, contrary to our expectations based on bacteria. Accumulated ppGpp was found to be present solely in the cytosolic fraction and not in the mitochondrial fraction, perhaps reflecting the ribosome-independent ppGpp synthesis in S. cerevisiae cells. Unlike bacterial inosine monophosphate (IMP) dehydrogenases, the IMP dehydrogenase of S. cerevisiae was insensitive to ppGpp. Microarray analysis showed that ppGpp accumulation gave rise to marked changes in gene expression, with both upregulation and downregulation, including changes in mitochondrial gene expression. The most prominent upregulation (38-fold) was detected in the hypothetical gene YBR072C-A of unknown function, followed by many other known stress-responsive genes. S. cerevisiae may provide new opportunities to uncover and analyse the ppGpp signalling system in eukaryotic cells.
Collapse
Affiliation(s)
- Kozo Ochi
- National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan.,Department of Life Science, Hiroshima Institute of Technology, Miyake 2-1-1, Saeki-ku, Hiroshima 731-5193, Japan
| | | | - Takashi Inaoka
- National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
| | - Akiyo Yamada
- Department of Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo, 184-8588, Japan
| | - Kohsuke Hashimoto
- Department of Life Science, Hiroshima Institute of Technology, Miyake 2-1-1, Saeki-ku, Hiroshima 731-5193, Japan
| | - Takeshi Hosaka
- International Young Researchers Empowerment Center, Shinshu University, 8304, Minamiminowa, Nagano 399-4598, Japan
| | - Susumu Okamoto
- National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
| | - Yoshihiro Ozeki
- Department of Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo, 184-8588, Japan
| |
Collapse
|
25
|
The universally conserved prokaryotic GTPases. Microbiol Mol Biol Rev 2012; 75:507-42, second and third pages of table of contents. [PMID: 21885683 DOI: 10.1128/mmbr.00009-11] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Members of the large superclass of P-loop GTPases share a core domain with a conserved three-dimensional structure. In eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. As targets of mutation and toxins, GTPases are involved in the pathogenesis of cancer and infectious diseases. In prokaryotes also, it is hard to overestimate the importance of GTPases in cell physiology. Numerous papers have shed new light on the role of bacterial GTPases in cell cycle regulation, ribosome assembly, the stress response, and other cellular processes. Moreover, bacterial GTPases have been identified as high-potential drug targets. A key paper published over 2 decades ago stated that, "It may never again be possible to capture [GTPases] in a family portrait" (H. R. Bourne, D. A. Sanders, and F. McCormick, Nature 348:125-132, 1990) and indeed, the last 20 years have seen a tremendous increase in publications on the subject. Sequence analysis identified 13 bacterial GTPases that are conserved in at least 75% of all bacterial species. We here provide an overview of these 13 protein subfamilies, covering their cellular functions as well as cellular localization and expression levels, three-dimensional structures, biochemical properties, and gene organization. Conserved roles in eukaryotic homologs will be discussed as well. A comprehensive overview summarizing current knowledge on prokaryotic GTPases will aid in further elucidating the function of these important proteins.
Collapse
|
26
|
McCormick JR, Flärdh K. Signals and regulators that govern Streptomyces development. FEMS Microbiol Rev 2012; 36:206-31. [PMID: 22092088 PMCID: PMC3285474 DOI: 10.1111/j.1574-6976.2011.00317.x] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 10/29/2011] [Accepted: 10/30/2011] [Indexed: 12/16/2022] Open
Abstract
Streptomyces coelicolor is the genetically best characterized species of a populous genus belonging to the gram-positive Actinobacteria. Streptomycetes are filamentous soil organisms, well known for the production of a plethora of biologically active secondary metabolic compounds. The Streptomyces developmental life cycle is uniquely complex and involves coordinated multicellular development with both physiological and morphological differentiation of several cell types, culminating in the production of secondary metabolites and dispersal of mature spores. This review presents a current appreciation of the signaling mechanisms used to orchestrate the decision to undergo morphological differentiation, and the regulators and regulatory networks that direct the intriguing development of multigenomic hyphae first to form specialized aerial hyphae and then to convert them into chains of dormant spores. This current view of S. coelicolor development is destined for rapid evolution as data from '-omics' studies shed light on gene regulatory networks, new genetic screens identify hitherto unknown players, and the resolution of our insights into the underlying cell biological processes steadily improve.
Collapse
Affiliation(s)
| | - Klas Flärdh
- Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
27
|
Polkinghorne A, Vaughan L. Chlamydia abortus YhbZ, a truncated Obg family GTPase, associates with the Escherichia coli large ribosomal subunit. Microb Pathog 2011; 50:200-6. [DOI: 10.1016/j.micpath.2010.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 12/08/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
|
28
|
Sasindran SJ, Saikolappan S, Scofield VL, Dhandayuthapani S. Biochemical and physiological characterization of the GTP-binding protein Obg of Mycobacterium tuberculosis. BMC Microbiol 2011; 11:43. [PMID: 21352546 PMCID: PMC3056739 DOI: 10.1186/1471-2180-11-43] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 02/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Obg is a highly conserved GTP-binding protein that has homologues in bacteria, archaea and eukaryotes. In bacteria, Obg proteins are essential for growth, and they participate in spore formation, stress adaptation, ribosome assembly and chromosomal partitioning. This study was undertaken to investigate the biochemical and physiological characteristics of Obg in Mycobacterium tuberculosis, which causes tuberculosis in humans. RESULTS We overexpressed M. tuberculosis Obg in Escherichia coli and then purified the protein. This protein binds to, hydrolyzes and is phosphorylated with GTP. An anti-Obg antiserum, raised against the purified Obg, detects a 55 kDa protein in immunoblots of M. tuberculosis extracts. Immunoblotting also discloses that cultured M. tuberculosis cells contain increased amounts of Obg in the late log phase and in the stationary phase. Obg is also associated with ribosomes in M. tuberculosis, and it is distributed to all three ribosomal fractions (30 S, 50 S and 70 S). Finally, yeast two-hybrid analysis reveals that Obg interacts with the stress protein UsfX, indicating that M. tuberculosis Obg, like other bacterial Obgs, is a stress related protein. CONCLUSIONS Although its GTP-hydrolyzing and phosphorylating activities resemble those of other bacterial Obg homologues, M. tuberculosis Obg differs from them in these respects: (a) preferential association with the bacterial membrane; (b) association with all three ribosomal subunits, and (c) binding to the stress protein UsfX, rather than to RelA. Generation of mutant alleles of Obg of M. tuberculosis, and their characterization in vivo, may provide additional insights regarding its role in this important human pathogen.
Collapse
Affiliation(s)
- Smitha J Sasindran
- Regional Academic Health Center and Department of Microbiology and Immunology, The University of Texas Health Science Center at San Antonio, Edinburg, Texas 78541, USA
| | | | | | | |
Collapse
|
29
|
Meena LS, Rajni. Cloning and characterization of engA, a GTP-binding protein from Mycobacterium tuberculosis H(37)Rv. Biologicals 2011; 39:94-9. [PMID: 21330151 DOI: 10.1016/j.biologicals.2011.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 11/26/2022] Open
Abstract
Guanine nucleotides are key signaling molecules and many members of the G-protein family bind and hydrolyze nucleotides, particularly GTP, and regulate intracellular level of GTP and GDP. EngA is one of the members of these universally conserved GTPases. Amino acid sequence alignment of EngA of Mycobacterium tuberculosis H(37)Rv with other homologous bacterial proteins have shown that EngA of M. tuberculosis H(37)Rv has significant homology with EngA of other bacteria. EngA protein has shown GTP-binding and GTP hydrolysis activities as intrinsic biochemical properties of protein and this serves as a base to further investigate the physiological significance of this protein in the pathogenesis mechanism of M. tuberculosis H(37)Rv. In this paper for the first time EngA GTP-binding protein of M. tuberculosis H(37)Rv was functionally characterized for its GTPase and GTP-hydrolyzing activity. GTPases such as era, obg, lepA, and FtsZ are vital for growth and development and specifically cellular functions of bacteria, in view of these observations it can be concluded that EngA GTPase can be further utilized for the study of its functional role in the pathogenesis of M. tuberculosis H(37)Rv.
Collapse
Affiliation(s)
- Laxman S Meena
- Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
| | | |
Collapse
|
30
|
Lee Y, Bang WY, Kim S, Lazar P, Kim CW, Bahk JD, Lee KW. Molecular modeling study for interaction between Bacillus subtilis Obg and Nucleotides. PLoS One 2010; 5:e12597. [PMID: 20830302 PMCID: PMC2935376 DOI: 10.1371/journal.pone.0012597] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 08/16/2010] [Indexed: 11/19/2022] Open
Abstract
The bacterial Obg proteins (Spo0B-associated GTP-binding protein) belong to the subfamily of P-loop GTPase proteins that contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain which is referred as the “Obg fold” and now it is considered as one of the new targets for antibacterial drug. When the Obg protein is associated with GTP, it becomes activated, because conformation of Obg fold changes due to the structural changes of GTPase switch elements in GTP binding site. In order to investigate the effects and structural changes in GTP bound to Obg and GTPase switch elements for activation, four different molecular dynamics (MD) simulations were performed with/without the three different nucleotides (GTP, GDP, and GDP + Pi) using the Bacillus subtilis Obg (BsObg) structure. The protein structures generated from the four different systems were compared using their representative structures. The pattern of Cα-Cα distance plot and angle between the two Obg fold domains of simulated apo form and each system (GTP, GDP, and GDP+Pi) were significantly different in the GTP-bound system from the others. The switch 2 element was significantly changed in GTP-bound system. Also root-mean-square fluctuation (RMSF) analysis revealed that the flexibility of the switch 2 element region was much higher than the others. This was caused by the characteristic binding mode of the nucleotides. When GTP was bound to Obg, its γ-phosphate oxygen was found to interact with the key residue (D212) of the switch 2 element, on the contrary there was no such interaction found in other systems. Based on the results, we were able to predict the possible binding conformation of the activated form of Obg with L13, which is essential for the assembly with ribosome.
Collapse
Affiliation(s)
- Yuno Lee
- Division of Applied Life Science, Environmental Biotechnology National Core Research Center, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongsangnam-do, Republic of Korea
| | - Woo Young Bang
- Division of Applied Life Science, Environmental Biotechnology National Core Research Center, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongsangnam-do, Republic of Korea
- Swine Science and Technology Center, Jinju National University, Jinju, Gyeongsangnam-do, Republic of Korea
| | - Songmi Kim
- Division of Applied Life Science, Environmental Biotechnology National Core Research Center, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongsangnam-do, Republic of Korea
| | - Prettina Lazar
- Division of Applied Life Science, Environmental Biotechnology National Core Research Center, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongsangnam-do, Republic of Korea
| | - Chul Wook Kim
- Swine Science and Technology Center, Jinju National University, Jinju, Gyeongsangnam-do, Republic of Korea
| | - Jeong Dong Bahk
- Division of Applied Life Science, Environmental Biotechnology National Core Research Center, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongsangnam-do, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Science, Environmental Biotechnology National Core Research Center, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongsangnam-do, Republic of Korea
- * E-mail:
| |
Collapse
|
31
|
|
32
|
Bang WY, Hata A, Jeong IS, Umeda T, Masuda T, Chen J, Yoko I, Suwastika IN, Kim DW, Im CH, Lee BH, Lee Y, Lee KW, Shiina T, Bahk JD. AtObgC, a plant ortholog of bacterial Obg, is a chloroplast-targeting GTPase essential for early embryogenesis. PLANT MOLECULAR BIOLOGY 2009; 71:379-90. [PMID: 19636801 DOI: 10.1007/s11103-009-9529-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 07/14/2009] [Indexed: 05/21/2023]
Abstract
Obg is a ribosome-associated GTPase essential for bacterial viability and is conserved in most organisms, from bacteria to eukaryotes. Obg is also expressed in plants, which predicts an important role for this molecule in plant viability; however, the functions of the plant Obg homologs have not been reported. Here, we first identified Arabidopsis AtObgC as a plant chloroplast-targeting Obg and elucidated its molecular biological and physiological properties. AtObgC encodes a plant-specific Obg GTPase that contains an N-terminal region for chloroplast targeting and has intrinsic GTP hydrolysis activity. A targeting assay using a few AtObgC N-terminal truncation mutants revealed that AtObgC localizes to chloroplasts and its transit peptide consists of more than 50 amino acid residues. Interestingly, GFP-fused full-length AtObgC exhibited a punctate staining pattern in chloroplasts of Arabidopsis protoplasts, which suggests a dimerization or multimerization of AtObgC. Moreover, its Obg fold was indispensable for the generation of the punctate staining pattern, and thus, was supposed to be important for such oligomerization of AtObgC by mediating the protein-protein interaction. In addition, the T-DNA insertion AtObgC null mutant exhibited an embryonic lethal phenotype that disturbed the early stage of embryogenesis. Altogether, our results provide a significant implication that AtObgC as a chloroplast targeting GTPase plays an important role at the early embryogenesis by exerting its function in chloroplast protein synthesis.
Collapse
Affiliation(s)
- Woo Young Bang
- Division of Applied Life Sciences (BK21 and EB-NCRC), Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Xie P, Zeng A, Qin Z. cmdABCDEF, a cluster of genes encoding membrane proteins for differentiation and antibiotic production in Streptomyces coelicolor A3(2). BMC Microbiol 2009; 9:157. [PMID: 19650935 PMCID: PMC2782261 DOI: 10.1186/1471-2180-9-157] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 08/04/2009] [Indexed: 12/12/2022] Open
Abstract
Background Streptomyces coelicolor is the most studied Streptomyces species and an excellent model for studying differentiation and antibiotic production. To date, many genes have been identified to be required for its differentiation (e.g. bld genes for aerial growth and whi genes for sporulation) and antibiotics production (including actII-orf4, redD, cdaR as pathway-specific regulatory genes and afsR, absA1/A2 as pleiotropic regulatory genes). Results A gene cluster containing six genes (SCO4126-4131) was proved to be co-transcribed in S. coelicolor. Deletions of cmdABCDEF (SCO4126-4131) displayed defective sporulation including formation of aberrant branches, and abnormalities in chromosome segregation and spore septation. Disruption mutants of apparently orthologous genes of S. lividans and S. avermitilis also showed defective sporulation, implying that the role of these genes is similar among Streptomyces. Transcription of cmdB, and therefore presumably of the whole operon, was regulated developmentally. Five of the encoded proteins (CmdA, C, D, E, F) were predicted membrane proteins. The other, CmdB, a predicted ATP/GTP-binding protein with an ABC-transporter-ATPase domain shown here to be essential for its function, was also located on the cell membrane. These results indicate that CmdABCDEF proteins mainly affect Streptomyces differentiation at an early stage of aerial hyphae formation, and suggest that these proteins may form a complex on cell membrane for proper segregation of chromosomes. In addition, deletions of cmdABCDEF also revealed over-production of blue-pigmented actinorhodin (Act) via activation of transcription of the pathway-specific regulatory gene actII-orf4 of actinorhodin biosynthesis. Conclusion In this study, six co-transcribed genes cmdABCDEF were identified by their effects on differentiation and antibiotic production in Streptomyces coelicolor A3(2). These six membrane-located proteins are possibly assembled into a complex to function.
Collapse
Affiliation(s)
- Pengfei Xie
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai, PR China.
| | | | | |
Collapse
|
34
|
Parente JA, Borges CL, Bailão AM, Felipe MSS, Pereira M, de Almeida Soares CM. Comparison of transcription of multiple genes during mycelia transition to yeast cells of Paracoccidioides brasiliensis reveals insights to fungal differentiation and pathogenesis. Mycopathologia 2008; 165:259-73. [PMID: 18777633 DOI: 10.1007/s11046-007-9078-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The ascomycete Paracoccidioides brasiliensis is a human pathogen with a broad distribution in Latin America. The infection process of P. brasiliensis is initiated by aerially dispersed mycelia propagules, which differentiate into the yeast parasitic phase in human lungs. Therefore, the transition to yeast is an initial and fundamental step in the infective process. In order to identify and characterize genes involved in P. brasiliensis transition to yeast, which could be potentially associated to early fungal adaptation to the host, expressed sequence tags (ESTs) were examined from a cDNA library, prepared from mycelia ongoing differentiation to yeast cells. In this study, it is presented a screen for a set of genes related to protein synthesis and to protein folding/modification/destination expressed during morphogenesis from mycelium to yeast. Our analysis revealed 43 genes that are induced during the early transition process, when compared to mycelia. In addition, eight novel genes related to those processes were described in the P. brasiliensis transition cDNA library. The types of induced and novel genes in the transition cDNA library highlight some metabolic aspects, such as putative increase in protein synthesis, in protein glycosylation, and in the control of protein folding that seem to be relevant to the fungal transition to the parasitic phase.
Collapse
Affiliation(s)
- Juliana Alves Parente
- Laboratório de Biologia Molecular, ICB II, Campus II, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
| | | | | | | | | | | |
Collapse
|
35
|
The growth-promoting and stress response activities of the Bacillus subtilis GTP binding protein Obg are separable by mutation. J Bacteriol 2008; 190:6625-35. [PMID: 18689482 DOI: 10.1128/jb.00799-08] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis Obg is a ribosome-associating GTP binding protein that is needed for growth, sporulation, and induction of the bacterium's general stress regulon (GSR). It is unclear whether the roles of Obg in sporulation and stress responsiveness are direct or a secondary effect of its growth-promoting functions. The present work addresses this question by an analysis of two obg alleles whose phenotypes argue for direct roles for Obg in each process. The first allele [obg(G92D)] encodes a missense change in the protein's highly conserved "obg fold" region. This mutation impairs cell growth and the ability of Obg to associate with ribosomes but fails to block sporulation or the induction of the GSR. The second obg mutation [obg(Delta22)] replaces the 22-amino-acid carboxy-terminal sequence of Obg with an alternative 26-amino-acid sequence. This Obg variant cofractionates with ribosomes and allows normal growth but blocks sporulation and impairs the induction of the GSR. Additional experiments revealed that the block on sporulation occurs early, preventing the activation of the essential sporulation transcription factor Spo0A, while inhibition of the GSR appears to involve a failure of the protein cascade that normally activates the GSR to effectively catalyze the reactions needed to activate the GSR transcription factor (sigma(B)).
Collapse
|
36
|
Functional analysis of the essential GTP-binding-protein-coding gene cgtA of Vibrio cholerae. J Bacteriol 2008; 190:4764-71. [PMID: 18456812 DOI: 10.1128/jb.02021-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cgtA gene, coding for the conserved G protein CgtA, is essential in bacteria. In contrast to a previous report, here we show by using genetic analysis that cgtA is essential in Vibrio cholerae even in a Delta relA background. Depletion of CgtA affected the growth of V. cholerae and rendered the cells highly sensitive to the replication inhibitor hydroxyurea. Overexpression of V. cholerae CgtA caused distinct elongation of Escherichia coli cells. Deletion analysis indicated that the C-terminal end of CgtA plays a critical role in its proper function.
Collapse
|
37
|
Cloning and characterization of GTP-binding proteins of Mycobacterium tuberculosis H37Rv. Enzyme Microb Technol 2008; 42:138-44. [DOI: 10.1016/j.enzmictec.2007.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 08/20/2007] [Accepted: 08/28/2007] [Indexed: 11/23/2022]
|
38
|
Abstract
GTPases are a universally conserved class of regulatory proteins involved in such diverse cellular functions as signal transduction, translation, cytoskeleton formation, and intracellular transport. GTPases are also required for ribosome assembly in eukaryotes and bacteria, where they present themselves as possible regulatory molecules. Strikingly, in bacteria they represent the largest class of essential assembly factors. A review of their common structural, biochemical and genetic interactions is presented and integrated with models for their function in ribosome assembly.
Collapse
Affiliation(s)
- Katrin Karbstein
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109-1055, USA.
| |
Collapse
|
39
|
Lapik YR, Misra JM, Lau LF, Pestov DG. Restricting conformational flexibility of the switch II region creates a dominant-inhibitory phenotype in Obg GTPase Nog1. Mol Cell Biol 2007; 27:7735-44. [PMID: 17785438 PMCID: PMC2169037 DOI: 10.1128/mcb.01161-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nog1 is a conserved eukaryotic GTPase of the Obg family involved in the biogenesis of 60S ribosomal subunits. Here we report the unique dominant-inhibitory properties of a point mutation in the switch II region of mouse Nog1; this mutation is predicted to restrict conformational mobility of the GTP-binding domain. We show that although the mutation does not significantly affect GTP binding, ectopic expression of the mutant in mouse cells disrupts productive assembly of pre-60S subunits and arrests cell proliferation. The mutant impairs processing of multiple pre-rRNA intermediates, resulting in the degradation of the newly synthesized 5.8S/28S rRNA precursors. Sedimentation analysis of nucleolar preribosomes indicates that defective Nog1 function inhibits the conversion of 32S pre-rRNA-containing complexes to a smaller form, resulting in a drastic accumulation of enlarged pre-60S particles in the nucleolus. These results suggest that conformational changes in the switch II element of Nog1 have a critical importance for the dissociation of preribosome-bound factors during intranucleolar maturation and thereby strongly influence the overall efficiency of the assembly process.
Collapse
Affiliation(s)
- Yevgeniya R Lapik
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago College of Medicine, Chicago, Illinois 60607, USA
| | | | | | | |
Collapse
|
40
|
Komatsu M, Takano H, Hiratsuka T, Ishigaki Y, Shimada K, Beppu T, Ueda K. Proteins encoded by the conservon of Streptomyces coelicolor A3(2) comprise a membrane-associated heterocomplex that resembles eukaryotic G protein-coupled regulatory system. Mol Microbiol 2007; 62:1534-46. [PMID: 17083469 DOI: 10.1111/j.1365-2958.2006.05461.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Streptomyces coelicolor A3(2) retains unique conserved operons termed conservons. Here, one of the conservons (cvn9), which encodes five proteins (A9-E9), was characterized. Mutants for cvnA9 and cvnAlO conditionally overproduced actinorhodin and performed precocious aerial growth, while a cvnE9 mutant showed the parental phenotype. Transcription of bidG, adpA and bldN was upregulated in the cvnA9 mutant. A9-D9 were detected in the insoluble fraction of cell-free extract of S. coelicolor by Western analysis. Biochemical analyses revealed that A9 has ATP-hydrolysing and adenine nucleotide-binding activities; D9 has GTP-hydrolysing and guanine nucleotide-binding activities; and E9 shows a typical spectrum similar to cytochrome P450. The comprehensive interaction assays demonstrated the occurrence of specific interactions between A9 and B9, A9 and C9, B9 and B9, B9 and D9, and C9 and D9. A9 associated with and dissociated from B9 (and C9) when ATP and ATP-gamma-S were supplied in the reaction respectively. Similarly, D9 associated with and dissociated from B9 (and C9) when GTP and GTP-gamma-S were supplied respectively. A9 and B9 were also shown for the occurrence as homocomplexes. Probably, Cvn9 proteins comprise a membrane-associated heterocomplex resembling the eukaryotic G-protein-coupled receptor system, which may serve as a signal transducer that connects to the bld cascade.
Collapse
Affiliation(s)
- Mamoru Komatsu
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-8510, Japan
| | | | | | | | | | | | | |
Collapse
|
41
|
Jiang M, Sullivan SM, Wout PK, Maddock JR. G-protein control of the ribosome-associated stress response protein SpoT. J Bacteriol 2007; 189:6140-7. [PMID: 17616600 PMCID: PMC1951942 DOI: 10.1128/jb.00315-07] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial response to stress is controlled by two proteins, RelA and SpoT. RelA generates the alarmone (p)ppGpp under amino acid starvation, whereas SpoT is responsible for (p)ppGpp hydrolysis and for synthesis of (p)ppGpp under a variety of cellular stress conditions. It is widely accepted that RelA is associated with translating ribosomes. The cellular location of SpoT, however, has been controversial. SpoT physically interacts with the ribosome-associated GTPase CgtA, and we show here that, under an optimized salt condition, SpoT is also associated with a pre-50S particle. Analysis of spoT and cgtA mutants and strains overexpressing CgtA suggests that the ribosome associations of SpoT and CgtA are mutually independent. The steady-state level of (p)ppGpp is increased in a cgtA mutant, but the accumulation of (p)ppGpp during amino acid starvation is not affected, providing strong evidence that CgtA regulates the (p)ppGpp level during exponential growth but not during the stringent response. We show that CgtA is not associated with pre-50S particles during amino acid starvation, indicating that under these conditions in which (p)ppGpp accumulates, CgtA is not bound either to the pre-50S particle or to SpoT. We propose that, in addition to its role as a 50S assembly factor, CgtA promotes SpoT (p)ppGpp degradation activity on the ribosome and that the loss of CgtA from the ribosome is necessary for maximal (p)ppGpp accumulation under stress conditions. Intriguingly, we found that in the absence of spoT and relA, cgtA is still an essential gene in Escherichia coli.
Collapse
Affiliation(s)
- Mengxi Jiang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
| | | | | | | |
Collapse
|
42
|
Abstract
Escherichia coli cells depleted of the conserved GTPase, ObgE, show early chromosome-partitioning defects and accumulate replicated chromosomes in which the terminus regions are colocalized. Cells lacking ObgE continue to initiate replication, with a normal ratio of the origin to terminus. Localization of the SeqA DNA binding protein, normally seen as punctate foci, however, was disturbed. Depletion of ObgE also results in cell filamentation, with polyploid DNA content. Depletion of ObgE did not cause lethality, and cells recovered fully after expression of ObgE was restored. We propose a model in which ObgE is required to license chromosome segregation and subsequent cell cycle events.
Collapse
Affiliation(s)
- James J Foti
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA
| | | | | | | |
Collapse
|
43
|
Taguchi T, Okamoto S, Lezhava A, Li A, Ochi K, Ebizuka Y, Ichinose K. Possible involvement of ActVI-ORFA in transcriptional regulation of actVI tailoring-step genes for actinorhodin biosynthesis. FEMS Microbiol Lett 2007; 269:234-9. [PMID: 17227452 DOI: 10.1111/j.1574-6968.2007.00627.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The actinorhodin biosynthetic gene (act) cluster in Streptomyces coelicolor carries a functionally unknown gene, actVI-ORFA. We have characterized an ActVI-ORFA disruptant by functional complementation and reverse transcriptase polymerase chain reaction analysis of the expression profiles of the act genes. Introduction of the functional actVI-ORFA gene into the disruptant restored actinorhodin production to an extent similar to that seen in the wild-type cells and abolished the accumulation of actinorhodin biosynthetic intermediates and shunt products specific for actVI mutants. Thus, unique phenotypes observed in the mutant are solely dependent on the function of actVI-ORFA. The disruptant was shown to yield significantly lower levels of the transcripts for certain act genes, especially for the actVI-ORF1-VA-ORF2 transcription unit, leading to the accumulation of the intermediates and shunt products. The functional actVI-ORFA gene restored expression of actVI-ORF1, which encodes a key reductase in the actinorhodin tailoring step, in the mutant cells, indicating a possible regulatory role of ActVI-ORFA.
Collapse
Affiliation(s)
- Takaaki Taguchi
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, Japan
| | | | | | | | | | | | | |
Collapse
|
44
|
Raskin DM, Judson N, Mekalanos JJ. Regulation of the stringent response is the essential function of the conserved bacterial G protein CgtA in Vibrio cholerae. Proc Natl Acad Sci U S A 2007; 104:4636-41. [PMID: 17360576 PMCID: PMC1838653 DOI: 10.1073/pnas.0611650104] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gene encoding the conserved bacterial G protein CgtA (Obg) is essential for viability in every organism in which it has been studied. CgtA has been reported to be involved in several diverse bacterial functions, including ribosome assembly, DNA repair, sporulation, and morphological development. However, none of these functions have been identified as essential. Here we show that depletion of CgtA in Vibrio cholerae causes global changes in gene expression that are consistent with induction of a classical low nutrient stress response or "stringent" response. We show that depletion of CgtA leads to increased ppGpp levels that correlate with induction of the global stress response and cessation of growth. The enzyme RelA is responsible for synthesis of the alarmone ppGpp during the stringent response. We show that CgtA is no longer essential in a relA deletion mutant and thus conclude that the essentiality of CgtA is directly linked to its ability to affect ppGpp levels. The enzyme SpoT degrades ppGpp, and here we show that SpoT is essential in a RelA+ CgtA+ background but not in a relA deletion mutant. We also confirmed that CgtA interacts with SpoT in a two-hybrid assay. We suggest that the essential function of CgtA is as a repressor of the stringent response that acts by regulating SpoT activity to maintain low ppGpp levels when bacteria are growing in a nutrient-rich environment.
Collapse
Affiliation(s)
- David M. Raskin
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - Nicholas Judson
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - John J. Mekalanos
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
45
|
Hirano Y, Ohniwa RL, Wada C, Yoshimura SH, Takeyasu K. Human small G proteins, ObgH1, and ObgH2, participate in the maintenance of mitochondria and nucleolar architectures. Genes Cells 2006; 11:1295-304. [PMID: 17054726 DOI: 10.1111/j.1365-2443.2006.01017.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Obg subfamily protein is one of the P-loop small G proteins and is highly conserved in many organisms from bacteria to human. Two obg genes, obgH1 and obgH2, exist in the human genome. Both ObgH1 and ObgH2 showed similar GTPase activities (0.014 +/- 0.005 and 0.010 +/- 0.002/min for ObgH1 and ObgH2, respectively) to those of the bacterial Obg proteins and complemented the Obg function in Escherichia coli ribosome maturation, suggesting that the functions of Obg proteins are well conserved through evolution. Immunofluorescence microscopy of HeLa cells revealed that ObgH1 localizes in mitochondria, and ObgH2 in the dense fibrillar compartment region of the nucleolus. Knock-down of ObgH1 by RNAi induced mitochondria elongation, whereas knock-down of ObgH2 resulted in the disorganization of the nucleolar architecture. In conclusion, the two human Obg proteins have similar enzymatic activities that can complement bacterial Obg function, but show different cellular function(s) with different intracellular localizations.
Collapse
Affiliation(s)
- Yasuhiro Hirano
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502 Japan.
| | | | | | | | | |
Collapse
|
46
|
Jiang M, Datta K, Walker A, Strahler J, Bagamasbad P, Andrews PC, Maddock JR. The Escherichia coli GTPase CgtAE is involved in late steps of large ribosome assembly. J Bacteriol 2006; 188:6757-70. [PMID: 16980477 PMCID: PMC1595513 DOI: 10.1128/jb.00444-06] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial ribosome is an extremely complicated macromolecular complex the in vivo biogenesis of which is poorly understood. Although several bona fide assembly factors have been identified, their precise functions and temporal relationships are not clearly defined. Here we describe the involvement of an Escherichia coli GTPase, CgtA(E), in late steps of large ribosomal subunit biogenesis. CgtA(E) belongs to the Obg/CgtA GTPase subfamily, whose highly conserved members are predominantly involved in ribosome function. Mutations in CgtA(E) cause both polysome and rRNA processing defects; small- and large-subunit precursor rRNAs accumulate in a cgtA(E) mutant. In this study we apply a new semiquantitative proteomic approach to show that CgtA(E) is required for optimal incorporation of certain late-assembly ribosomal proteins into the large ribosomal subunit. Moreover, we demonstrate the interaction with the 50S ribosomal subunits of specific nonribosomal proteins (including heretofore uncharacterized proteins) and define possible temporal relationships between these proteins and CgtA(E). We also show that purified CgtA(E) associates with purified ribosomal particles in the GTP-bound form. Finally, CgtA(E) cofractionates with the mature 50S but not with intermediate particles accumulated in other large ribosome assembly mutants.
Collapse
Affiliation(s)
- Mengxi Jiang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Saito N, Xu J, Hosaka T, Okamoto S, Aoki H, Bibb MJ, Ochi K. EshA accentuates ppGpp accumulation and is conditionally required for antibiotic production in Streptomyces coelicolor A3(2). J Bacteriol 2006; 188:4952-61. [PMID: 16788203 PMCID: PMC1483009 DOI: 10.1128/jb.00343-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Disruption of eshA, which encodes a 52-kDa protein that is produced late during the growth of Streptomyces coelicolor A3(2), resulted in elimination of actinorhodin production. In contrast, disruption of eshB, a close homologue of eshA, had no effect on antibiotic production. The eshA disruptant accumulated lower levels of ppGpp than the wild-type strain accumulated. The loss of actinorhodin production in the eshA disruptant was restored by expression of a truncated relA gene, which increased the ppGpp level to the level in the wild-type strain, indicating that the reduced ppGpp accumulation in the eshA mutant was solely responsible for the loss of antibiotic production. Antibiotic production was also restored in the eshA mutant by introducing mutations into rpoB (encoding the RNA polymerase beta subunit) that bypassed the requirement for ppGpp, which is consistent with a role for EshA in modulating ppGpp levels. EshA contains a cyclic nucleotide-binding domain that is essential for its role in triggering actinorhodin production. EshA may provide new insights and opportunities to unravel the molecular signaling events that occur during physiological differentiation in streptomycetes.
Collapse
Affiliation(s)
- Natsumi Saito
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | | | | | | | | | | | | |
Collapse
|
48
|
Hosaka T, Xu J, Ochi K. Increased expression of ribosome recycling factor is responsible for the enhanced protein synthesis during the late growth phase in an antibiotic-overproducing Streptomyces coelicolor ribosomal rpsL mutant. Mol Microbiol 2006; 61:883-97. [PMID: 16859496 DOI: 10.1111/j.1365-2958.2006.05285.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
K88E mutation within rpsL, which encodes the S12 ribosomal protein, enhanced the protein synthetic activity of Streptomyces coelicolor during the late growth phase, resulting in overproduction of the deep blue-pigmented polyketide antibiotic actinorhodin. In vitro cross-mixing experiments using the ribosomal and S-150 fractions derived from wild-type and K88E mutant strains suggested that one or more translation factors are enriched in the mutant's S-150 fraction, while Western analysis using antibodies against various translation factors revealed ribosome recycling factor (RRF) to be one of the enriched mediators. RRF purified from overexpressing cells stimulated mRNA-directed green fluorescent protein (GFP) synthesis in an in vitro protein synthesis system. GFP synthesis rates were complemented by RRF addition into wild-type cell's S-150 fraction, eliminating the difference between wild-type and mutant S-150 fractions. The frr gene encoding RRF was found to be transcribed from two distinct start points (frrp1 and frrp2), and increased expression from frrp1 could account for the elevated level of RRF in the K88E mutant during the late growth phase. Moreover, introduction of a plasmid harbouring a high copy number of frr gene into wild-type S. coelicolor induced remarkable overproduction of antibiotic, demonstrating that the increased levels of RRF caused by the K88E mutation is responsible for an aberrant stationary-phase event: overproduction of antibiotic.
Collapse
Affiliation(s)
- Takeshi Hosaka
- National Food Research Institute, Tsukuba, Ibaraki, Japan
| | | | | |
Collapse
|
49
|
Di Cagno R, De Angelis M, Limitone A, Fox PF, Gobbetti M. Response of Lactobacillus helveticus PR4 to heat stress during propagation in cheese whey with a gradient of decreasing temperatures. Appl Environ Microbiol 2006; 72:4503-14. [PMID: 16820437 PMCID: PMC1489348 DOI: 10.1128/aem.01829-05] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 03/16/2006] [Indexed: 11/20/2022] Open
Abstract
The heat stress response was studied in Lactobacillus helveticus PR4 during propagation in cheese whey with a gradient of naturally decreasing temperature (55 to 20 degrees C). Growth under a gradient of decreasing temperature was compared to growth at a constant temperature of 42 degrees C. Proteinase, peptidase, and acidification activities of L. helveticus PR4 were found to be higher in cells harvested when 40 degrees C was reached by a gradient of decreasing temperature than in cells grown at constant temperature of 42 degrees C. When cells grown under a temperature gradient were harvested after an initial exposure of 35 min to 55 degrees C followed by decreases in temperature to 40 (3 h), 30 (5 h 30 min), or 20 degrees C (13 h 30 min) and were then compared with cells grown for the same time at a constant temperature of 42 degrees C, a frequently transient induction of the levels of expression of 48 proteins was found by two-dimensional electrophoresis analysis. Expression of most of these proteins increased following cooling from 55 to 40 degrees C (3 h). Sixteen of these proteins were subjected to N-terminal and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses. They were identified as stress proteins (e.g., DnaK and GroEL), glycolysis-related machinery (e.g., enolase and glyceraldehyde-3-phosphate dehydrogenase), and other regulatory proteins or factors (e.g., DNA-binding protein II and ATP-dependent protease). Most of these proteins have been found to play a role in the mechanisms of heat stress adaptation in other bacteria.
Collapse
Affiliation(s)
- Raffaella Di Cagno
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Facoltà di Scienze Biotecnologiche di Bari, Via G. Amendola 165/a, 70126 Bari, Italy
| | | | | | | | | |
Collapse
|
50
|
Sikora AE, Zielke R, Datta K, Maddock JR. The Vibrio harveyi GTPase CgtAV is essential and is associated with the 50S ribosomal subunit. J Bacteriol 2006; 188:1205-10. [PMID: 16428430 PMCID: PMC1347350 DOI: 10.1128/jb.188.3.1205-1210.2006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It was previously reported that unlike the other obg/cgtA GTPases, the Vibrio harveyi cgtAV is not essential. Here we show that cgtAV was not disrupted in these studies and is, in fact, essential for viability. Depletion of CgtAV did not result in cell elongation. CgtAV is associated with the large ribosomal particle. In light of our results, we predict that the V. harveyi CgtAV protein plays a similar essential role to that seen for Obg/CgtA proteins in other bacteria.
Collapse
Affiliation(s)
- A E Sikora
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
| | | | | | | |
Collapse
|